How does the lens degrade one type of movie, but not the other? If anything, you'd expect a 2D presentation on a stereoscopic setup to be too bright due to not having half the light blocked by glasses.
All I can think of is these two things happening simultaneously:
1) They're using the same amount of light to project stereoscopic as they would for normal 2D. This would cause "3D" movies to be too dim as well. Maybe stereoscopic movies are pre-processed to compensate.
2) 2D movies only get projected through the left (or right) lens. The other lens projects "black" or, more accurately, a dark shade of grey.